circrnaPrepareFiles: Function to prepare the CircHunter reference annotations

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Function to prepare the CircHunter reference annotations

Description

This function executes the docker container circhunter by running the circRNA classification module of CircHunter starting from a set of circRNAs. For CircHunter algorithm detail please refer to: https://github.com/carlo-deintinis/circhunter/tree/master/CircHunter.

Usage

circrnaPrepareFiles(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  assembly = "hg19",
  version = NULL
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
data.folder	a character string indicating the data folder where the output files will be saved
assembly	string indicating the reference human genome assembly. Compatible assemblies: hg19 (default), hg18, hg38, mm9, mm10, rn6, dm6, ce11
version	Ensembl database version used for the analysis. If no version number is provided, the last version is considered

Value

Two tab-delimited tables reporting the exons and the transcript isoforms annotations of an user-selected human genome assembly

Author(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 
    #Download the example data
    system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip")
    system("unzip master.zip")

    #running the circrnaPrepareFiles function
    circrnaPrepareFiles(group="docker", scratch.folder="/data/scratch", data.folder="/data/output", assembly="hg19")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.